Deep learning linking mechanistic models to single-cell transcriptomics data reveals transcriptional bursting in response to DNA damage
Identification
- Clé publique
- radar:r-47423407215d5d7a4a16e36cc5b298b2
- Auteurs
- Zhiwei Huang · Songhao Luo · Z. Wang · Zhenquan Zhang · Benyuan Jiang · Qing Hua Nie · Jiajun Zhang
- Année déclarée
- 2026
- Langue déclarée
- en
- Type source
- preprint
- Première détection
- 2026-11-14T02:03:31.399789+00:00
- Dernière observation des métadonnées
- 2026-11-14T02:03:31.399789+00:00
- Dernière vérification HTTP
- Non effectuée
Institutions déclarées par la source
Sun Yat-sen University · Guangdong Province Key Laboratory of Computational Science · University of California, Irvine · Guangdong Academy of Medical Sciences · Guangdong Provincial People's Hospital
Pays d’affiliation déclarés
CN · US
Résumé documentaire — langue originale
Cells must adopt flexible regulatory strategies to make decisions regarding their fate, including differentiation, apoptosis, or survival in the face of various external stimuli. One key cellular strategy that enables these functions is stochastic gene expression programs. However, understanding how transcriptional bursting, and consequently, cell fate, responds to DNA damage on a genome-wide scale poses a challenge. In this study, we propose an interpretable and scalable inference framework, DeepTX, that leverages deep learning methods to connect mechanistic models and scRNA-seq data, thereby revealing genome-wide transcriptional burst kinetics. This framework enables rapid and accurate solutions to transcription models and the inference of transcriptional burst kinetics from scRNA-seq data. Applying this framework to several scRNA-seq datasets of DNA-damaging drug treatments, we observed that fluctuations in transcriptional bursting induced by different drugs was associated with distinct fate decisions: IdU treatment was associated with differentiation in mouse embryonic stem cells by increasing the burst size of gene expression, while low- and high-dose 5FU treatments in human colon cancer cells were associated with changes in burst frequency that corresponded to apoptosis- and survival-related fate, respectively. Together, these results show that DeepTX enables genome-wide inference of transcriptional bursting from single-cell transcriptomics data and can generate hypotheses about how bursting dynamics relate to cell fate decisions.
Identifiants
- OPENALEX
- https://openalex.org/W7124455962
- DOI
- 10.7554/elife.100623.3
Repères documentaires
- Famille documentaire
- preprint
- Types déclarés par les sources
- preprint
- Éditeurs
- eLife Sciences Publications Ltd
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Sources
OpenAlex · Document 1
Citer cette référence
Zhiwei Huang; Songhao Luo; Z. Wang; Zhenquan Zhang; Benyuan Jiang; Qing Hua Nie; Jiajun Zhang. Deep learning linking mechanistic models to single-cell transcriptomics data reveals transcriptional bursting in response to DNA damage. 2026. https://doi.org/10.7554/elife.100623.3
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- APA
- Zhiwei Huang; Songhao Luo; Z. Wang; Zhenquan Zhang; Benyuan Jiang; Qing Hua Nie; Jiajun Zhang. (2026). Deep learning linking mechanistic models to single-cell transcriptomics data reveals transcriptional bursting in response to DNA damage. https://doi.org/10.7554/elife.100623.3
- Chicago
- Zhiwei Huang; Songhao Luo; Z. Wang; Zhenquan Zhang; Benyuan Jiang; Qing Hua Nie; Jiajun Zhang. Deep learning linking mechanistic models to single-cell transcriptomics data reveals transcriptional bursting in response to DNA damage. 2026. https://doi.org/10.7554/elife.100623.3
- ISO 690
- Zhiwei Huang; Songhao Luo; Z. Wang; Zhenquan Zhang; Benyuan Jiang; Qing Hua Nie; Jiajun Zhang. Deep learning linking mechanistic models to single-cell transcriptomics data reveals transcriptional bursting in response to DNA damage. 2026. https://doi.org/10.7554/elife.100623.3
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Source bibliographique / publication d’origine · https://doi.org/10.7554/elife.100623.3
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